This document compares the results of at least 2 CASAL model configurations (base and at least one sensitivity) and up to 8 Casal2 model configurations (3 BetaDiff, 2 CppAD, and 3 ADOL-C).
The CASAL model sensitivity 1 has a smaller minimisation tolerance value than the CASAL base model (1e-8 vs. 2e-6).
The Casal2 ADOL-C and BetaDiff low tolerance models have a smaller tolerance value than the CASAL base model (1e-8 vs. 2e-6). The Casal2 CppAD models have a tolerance value of 1e-9.
The main characteristics of the Test Case SBW (southern blue whiting) CASAL model are:
Observation data include:
Parameters estimated include:
## [1] "Mon Nov 23 15:50:01 2020"
## R version 3.6.0 (2019-04-26)
## Platform: x86_64-redhat-linux-gnu (64-bit)
## Running under: CentOS Linux 7 (Core)
##
## Matrix products: default
## BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so
##
## locale:
## [1] LC_CTYPE=en_NZ.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_NZ.UTF-8 LC_COLLATE=en_NZ.UTF-8
## [5] LC_MONETARY=en_NZ.UTF-8 LC_MESSAGES=en_NZ.UTF-8
## [7] LC_PAPER=en_GB.UTF_8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_NZ.UTF-8 LC_IDENTIFICATION=C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] casal2_1.0 casal_2.30 ggthemes_4.2.0 ggmcmc_1.5.0 tidyr_1.1.2
## [6] ggplot2_3.3.2 gridExtra_2.3 coda_0.19-4 rlist_0.4.6.1 huxtable_5.1.1
## [11] dplyr_1.0.2 plyr_1.8.6 devtools_2.3.2 usethis_1.6.3
##
## loaded via a namespace (and not attached):
## [1] tidyselect_1.1.0 xfun_0.19 remotes_2.2.0 purrr_0.3.4
## [5] lattice_0.20-38 colorspace_1.4-1 vctrs_0.3.5 generics_0.1.0
## [9] testthat_2.3.2 htmltools_0.5.0 yaml_2.2.1 rlang_0.4.8
## [13] pkgbuild_1.1.0 pillar_1.4.7 glue_1.4.2 withr_2.3.0
## [17] RColorBrewer_1.1-2 sessioninfo_1.1.1 lifecycle_0.2.0 stringr_1.4.0
## [21] munsell_0.5.0 gtable_0.3.0 memoise_1.1.0 evaluate_0.14
## [25] GGally_1.4.0 knitr_1.30 callr_3.5.1 ps_1.4.0
## [29] fansi_0.4.1 Rcpp_1.0.5 scales_1.1.1 desc_1.2.0
## [33] pkgload_1.1.0 fs_1.5.0 digest_0.6.27 stringi_1.5.3
## [37] processx_3.4.4 rprojroot_2.0.2 grid_3.6.0 cli_2.2.0
## [41] tools_3.6.0 magrittr_2.0.1 tibble_3.0.4 crayon_1.3.4
## [45] pkgconfig_2.0.3 ellipsis_0.3.1 data.table_1.13.2 prettyunits_1.1.1
## [49] reshape_0.8.8 assertthat_0.2.1 rmarkdown_2.5 R6_2.5.0
## [53] compiler_3.6.0
source('../../R-functions/report_read_in_CASAL_MPD_files.R')
source('../../R-functions/report_read_in_Casal2_MPD_files.R')
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(data): diag(.) had 0 or NA entries; non-finite result is
## doubtful
## Warning in sqrt(1/diag(V)): NaNs produced
## Warning in cov2cor(data): diag(.) had 0 or NA entries; non-finite result is
## doubtful
Tables of parameter estimates and objective function components for the CASAL and Casal2 model MPD results
| rownames | Base_Model | Sensitivity_1 | Percent_Diff |
|---|---|---|---|
| initialization.B0 | 314500.00000 | 314500.00000 | 0.000 |
| relative_abundance[TangaroaAcousticMature].cv_process_error | 0.00010 | 0.00010 | 0.000 |
| natural_mortality.avg | 0.15580 | 0.15580 | 0.000 |
| natural_mortality.diff | -0.00914 | -0.00914 | 0.000 |
| migration[toSpawn].rates_male1 | 0.08558 | 0.08558 | 0.000 |
| migration[toSpawn].rates_male2 | 0.72990 | 0.72990 | 0.000 |
| migration[toSpawn].rates_male3 | 0.51270 | 0.51270 | 0.000 |
| migration[toSpawn].rates_male4 | 0.33120 | 0.33120 | 0.000 |
| migration[toSpawn].rates_male5 | 0.99000 | 0.99000 | 0.000 |
| migration[toSpawn].rates_female1 | 0.01907 | 0.01907 | 0.000 |
| migration[toSpawn].rates_female2 | 0.51250 | 0.51250 | 0.000 |
| migration[toSpawn].rates_female3 | 0.94120 | 0.94120 | 0.000 |
| migration[toSpawn].rates_female4 | 0.99900 | 0.99900 | 0.000 |
| migration[toSpawn].rates_female5 | 0.99000 | 0.99000 | 0.000 |
| recruitment.YCS1 | 0.25590 | 0.25590 | 0.000 |
| recruitment.YCS2 | 0.26100 | 0.26100 | 0.000 |
| recruitment.YCS3 | 0.26700 | 0.26700 | 0.000 |
| recruitment.YCS4 | 0.27430 | 0.27430 | 0.000 |
| recruitment.YCS5 | 0.28320 | 0.28320 | 0.000 |
| recruitment.YCS6 | 0.29410 | 0.29410 | 0.000 |
| recruitment.YCS7 | 0.30880 | 0.30880 | 0.000 |
| recruitment.YCS8 | 0.82470 | 0.82470 | 0.000 |
| recruitment.YCS9 | 0.53160 | 0.53160 | 0.000 |
| recruitment.YCS10 | 0.37070 | 0.37070 | 0.000 |
| recruitment.YCS11 | 0.26680 | 0.26680 | 0.000 |
| recruitment.YCS12 | 0.13850 | 0.13850 | 0.000 |
| recruitment.YCS13 | 0.08025 | 0.08025 | 0.000 |
| recruitment.YCS14 | 0.15820 | 0.15820 | 0.000 |
| recruitment.YCS15 | 0.10630 | 0.10630 | 0.000 |
| recruitment.YCS16 | 0.05757 | 0.05757 | 0.000 |
| recruitment.YCS17 | 0.06079 | 0.06079 | 0.000 |
| recruitment.YCS18 | 0.12720 | 0.12720 | 0.000 |
| recruitment.YCS19 | 0.05057 | 0.05057 | 0.000 |
| recruitment.YCS20 | 0.03959 | 0.03959 | 0.000 |
| recruitment.YCS21 | 0.04996 | 0.04996 | 0.000 |
| recruitment.YCS22 | 0.37590 | 0.37590 | 0.000 |
| recruitment.YCS23 | 0.36820 | 0.36820 | 0.000 |
| recruitment.YCS24 | 0.09402 | 0.09402 | 0.000 |
| recruitment.YCS25 | 0.03280 | 0.03280 | 0.000 |
| recruitment.YCS26 | 0.13650 | 0.13650 | 0.000 |
| recruitment.YCS27 | 0.13080 | 0.13080 | 0.000 |
| recruitment.YCS28 | 0.11260 | 0.11260 | 0.000 |
| recruitment.YCS29 | 0.28620 | 0.28620 | 0.000 |
| recruitment.YCS30 | 0.12790 | 0.12790 | 0.000 |
| recruitment.YCS31 | 0.43770 | 0.43770 | 0.000 |
| recruitment.YCS32 | 0.03590 | 0.03590 | 0.000 |
| recruitment.YCS33 | 0.25650 | 0.25650 | 0.000 |
| recruitment.YCS34 | 2.75100 | 2.75100 | 0.000 |
| recruitment.YCS35 | 0.55870 | 0.55870 | 0.000 |
| recruitment.YCS36 | 0.26390 | 0.26390 | 0.000 |
| recruitment.YCS37 | 0.12670 | 0.12670 | 0.000 |
| recruitment.YCS38 | 0.56000 | 0.56000 | 0.000 |
| recruitment.YCS39 | 0.36190 | 0.36190 | 0.000 |
| recruitment.YCS40 | 0.14490 | 0.14490 | 0.000 |
| recruitment.YCS41 | 0.32060 | 0.32060 | 0.000 |
| recruitment.YCS42 | 0.19280 | 0.19280 | 0.000 |
| recruitment.YCS43 | 0.29870 | 0.29870 | 0.000 |
| recruitment.YCS44 | 0.70520 | 0.70520 | 0.000 |
| recruitment.YCS45 | 0.41770 | 0.41770 | 0.000 |
| recruitment.YCS46 | 0.25430 | 0.25430 | 0.000 |
| recruitment.YCS47 | 0.25240 | 0.25240 | 0.000 |
| recruitment.YCS48 | 0.32500 | 0.32500 | 0.000 |
| recruitment.YCS49 | 1.69600 | 1.69600 | 0.000 |
| recruitment.YCS50 | 0.68660 | 0.68660 | 0.000 |
| recruitment.YCS51 | 0.20070 | 0.20070 | 0.000 |
| recruitment.YCS52 | 1.20400 | 1.20400 | 0.000 |
| recruitment.YCS53 | 0.16930 | 0.16930 | 0.000 |
| recruitment.YCS54 | 0.87570 | 0.87570 | 0.000 |
| recruitment.YCS55 | 0.13270 | 0.13270 | 0.000 |
| recruitment.YCS56 | 1.00000 | 1.00000 | 0.000 |
| rownames | betadiff_casal_flags_on | betadiff_casal_flags_off | betadiff_casal_flags_on_low_tol | cppad_casal_flags_on | cppad_casal_flags_off | adolc_casal_flags_on | adolc_casal_flags_off | adolc_casal_flags_on_low_tol |
|---|---|---|---|---|---|---|---|---|
| process[Recruitment].b0 | 299610.00000 | 299610.00000 | 299610.00000 | 314527.00000 | 314527.00000 | 299610.00000 | 299610.00000 | 299610.00000 |
| selectivity[MaturationSel_male].v{1} | 0.08537 | 0.08537 | 0.08537 | 0.08558 | 0.08558 | 0.08537 | 0.08537 | 0.08537 |
| selectivity[MaturationSel_male].v{2} | 0.73526 | 0.73526 | 0.73526 | 0.72993 | 0.72993 | 0.73526 | 0.73526 | 0.73526 |
| selectivity[MaturationSel_male].v{3} | 0.51432 | 0.51432 | 0.51432 | 0.51267 | 0.51267 | 0.51432 | 0.51432 | 0.51432 |
| selectivity[MaturationSel_male].v{4} | 0.29398 | 0.29398 | 0.29398 | 0.33118 | 0.33118 | 0.29398 | 0.29398 | 0.29398 |
| selectivity[MaturationSel_female].v{1} | 0.01903 | 0.01903 | 0.01903 | 0.01907 | 0.01907 | 0.01903 | 0.01903 | 0.01903 |
| selectivity[MaturationSel_female].v{2} | 0.51564 | 0.51564 | 0.51564 | 0.51254 | 0.51254 | 0.51564 | 0.51564 | 0.51564 |
| selectivity[MaturationSel_female].v{3} | 0.94578 | 0.94578 | 0.94578 | 0.94120 | 0.94120 | 0.94578 | 0.94578 | 0.94578 |
| selectivity[MaturationSel_female].v{4} | 0.99900 | 0.99900 | 0.99900 | 0.99900 | 0.99900 | 0.99900 | 0.99900 | 0.99900 |
| process[Recruitment].ycs_values{1958} | 0.25169 | 0.25169 | 0.25169 | 0.25590 | 0.25590 | 0.25169 | 0.25169 | 0.25169 |
| process[Recruitment].ycs_values{1959} | 0.25626 | 0.25626 | 0.25626 | 0.26099 | 0.26099 | 0.25626 | 0.25626 | 0.25626 |
| process[Recruitment].ycs_values{1960} | 0.26170 | 0.26170 | 0.26170 | 0.26702 | 0.26702 | 0.26170 | 0.26170 | 0.26170 |
| process[Recruitment].ycs_values{1961} | 0.26830 | 0.26830 | 0.26830 | 0.27431 | 0.27431 | 0.26830 | 0.26830 | 0.26830 |
| process[Recruitment].ycs_values{1962} | 0.27632 | 0.27632 | 0.27632 | 0.28317 | 0.28317 | 0.27632 | 0.27632 | 0.27632 |
| process[Recruitment].ycs_values{1963} | 0.28636 | 0.28636 | 0.28636 | 0.29410 | 0.29410 | 0.28636 | 0.28636 | 0.28636 |
| process[Recruitment].ycs_values{1964} | 0.30009 | 0.30009 | 0.30009 | 0.30880 | 0.30880 | 0.30009 | 0.30009 | 0.30009 |
| process[Recruitment].ycs_values{1965} | 0.70701 | 0.70701 | 0.70701 | 0.82468 | 0.82468 | 0.70701 | 0.70701 | 0.70701 |
| process[Recruitment].ycs_values{1966} | 0.46402 | 0.46402 | 0.46402 | 0.53162 | 0.53162 | 0.46402 | 0.46402 | 0.46402 |
| process[Recruitment].ycs_values{1967} | 0.32237 | 0.32237 | 0.32237 | 0.37070 | 0.37070 | 0.32237 | 0.32237 | 0.32237 |
| process[Recruitment].ycs_values{1968} | 0.23172 | 0.23172 | 0.23172 | 0.26676 | 0.26676 | 0.23172 | 0.23172 | 0.23172 |
| process[Recruitment].ycs_values{1969} | 0.12143 | 0.12143 | 0.12143 | 0.13853 | 0.13853 | 0.12143 | 0.12143 | 0.12143 |
| process[Recruitment].ycs_values{1970} | 0.07084 | 0.07084 | 0.07084 | 0.08025 | 0.08025 | 0.07084 | 0.07084 | 0.07084 |
| process[Recruitment].ycs_values{1971} | 0.13612 | 0.13612 | 0.13612 | 0.15822 | 0.15822 | 0.13612 | 0.13612 | 0.13612 |
| process[Recruitment].ycs_values{1972} | 0.09151 | 0.09151 | 0.09151 | 0.10630 | 0.10630 | 0.09151 | 0.09151 | 0.09151 |
| process[Recruitment].ycs_values{1973} | 0.04983 | 0.04983 | 0.04983 | 0.05757 | 0.05757 | 0.04983 | 0.04983 | 0.04983 |
| process[Recruitment].ycs_values{1974} | 0.05215 | 0.05215 | 0.05215 | 0.06079 | 0.06079 | 0.05215 | 0.05215 | 0.05215 |
| process[Recruitment].ycs_values{1975} | 0.10750 | 0.10750 | 0.10750 | 0.12725 | 0.12725 | 0.10750 | 0.10750 | 0.10750 |
| process[Recruitment].ycs_values{1976} | 0.04308 | 0.04308 | 0.04308 | 0.05057 | 0.05057 | 0.04308 | 0.04308 | 0.04308 |
| process[Recruitment].ycs_values{1977} | 0.03373 | 0.03373 | 0.03373 | 0.03959 | 0.03959 | 0.03373 | 0.03373 | 0.03373 |
| process[Recruitment].ycs_values{1978} | 0.04227 | 0.04227 | 0.04227 | 0.04996 | 0.04996 | 0.04227 | 0.04227 | 0.04227 |
| process[Recruitment].ycs_values{1979} | 0.31277 | 0.31277 | 0.31277 | 0.37587 | 0.37587 | 0.31277 | 0.31277 | 0.31277 |
| process[Recruitment].ycs_values{1980} | 0.30480 | 0.30480 | 0.30480 | 0.36816 | 0.36816 | 0.30480 | 0.30480 | 0.30480 |
| process[Recruitment].ycs_values{1981} | 0.07799 | 0.07799 | 0.07799 | 0.09402 | 0.09402 | 0.07799 | 0.07799 | 0.07799 |
| process[Recruitment].ycs_values{1982} | 0.02751 | 0.02751 | 0.02751 | 0.03280 | 0.03280 | 0.02751 | 0.02751 | 0.02751 |
| process[Recruitment].ycs_values{1983} | 0.11248 | 0.11248 | 0.11248 | 0.13647 | 0.13647 | 0.11248 | 0.11248 | 0.11248 |
| process[Recruitment].ycs_values{1984} | 0.10757 | 0.10757 | 0.10757 | 0.13080 | 0.13080 | 0.10757 | 0.10757 | 0.10757 |
| process[Recruitment].ycs_values{1985} | 0.09256 | 0.09256 | 0.09256 | 0.11256 | 0.11256 | 0.09256 | 0.09256 | 0.09256 |
| process[Recruitment].ycs_values{1986} | 0.23474 | 0.23474 | 0.23474 | 0.28616 | 0.28616 | 0.23474 | 0.23474 | 0.23474 |
| process[Recruitment].ycs_values{1987} | 0.10518 | 0.10518 | 0.10518 | 0.12793 | 0.12793 | 0.10518 | 0.10518 | 0.10518 |
| process[Recruitment].ycs_values{1988} | 0.35849 | 0.35849 | 0.35849 | 0.43772 | 0.43772 | 0.35849 | 0.35849 | 0.35849 |
| process[Recruitment].ycs_values{1989} | 0.03001 | 0.03001 | 0.03001 | 0.03590 | 0.03590 | 0.03001 | 0.03001 | 0.03001 |
| process[Recruitment].ycs_values{1990} | 0.21160 | 0.21160 | 0.21160 | 0.25649 | 0.25649 | 0.21160 | 0.21160 | 0.21160 |
| process[Recruitment].ycs_values{1991} | 2.26862 | 2.26862 | 2.26862 | 2.75116 | 2.75116 | 2.26862 | 2.26862 | 2.26862 |
| process[Recruitment].ycs_values{1992} | 0.46042 | 0.46042 | 0.46042 | 0.55871 | 0.55871 | 0.46042 | 0.46042 | 0.46042 |
| process[Recruitment].ycs_values{1993} | 0.21818 | 0.21818 | 0.21818 | 0.26390 | 0.26390 | 0.21818 | 0.21818 | 0.21818 |
| process[Recruitment].ycs_values{1994} | 0.10632 | 0.10632 | 0.10632 | 0.12675 | 0.12675 | 0.10632 | 0.10632 | 0.10632 |
| process[Recruitment].ycs_values{1995} | 0.46220 | 0.46220 | 0.46220 | 0.56002 | 0.56002 | 0.46220 | 0.46220 | 0.46220 |
| process[Recruitment].ycs_values{1996} | 0.29958 | 0.29958 | 0.29958 | 0.36192 | 0.36192 | 0.29958 | 0.29958 | 0.29958 |
| process[Recruitment].ycs_values{1997} | 0.12096 | 0.12096 | 0.12096 | 0.14486 | 0.14486 | 0.12096 | 0.12096 | 0.12096 |
| process[Recruitment].ycs_values{1998} | 0.26476 | 0.26476 | 0.26476 | 0.32060 | 0.32060 | 0.26476 | 0.26476 | 0.26476 |
| process[Recruitment].ycs_values{1999} | 0.16048 | 0.16048 | 0.16048 | 0.19279 | 0.19279 | 0.16048 | 0.16048 | 0.16048 |
| process[Recruitment].ycs_values{2000} | 0.24624 | 0.24624 | 0.24624 | 0.29874 | 0.29874 | 0.24624 | 0.24624 | 0.24624 |
| process[Recruitment].ycs_values{2001} | 0.57498 | 0.57498 | 0.57498 | 0.70518 | 0.70518 | 0.57498 | 0.57498 | 0.57498 |
| process[Recruitment].ycs_values{2002} | 0.33816 | 0.33816 | 0.33816 | 0.41769 | 0.41769 | 0.33816 | 0.33816 | 0.33816 |
| process[Recruitment].ycs_values{2003} | 0.20585 | 0.20585 | 0.20585 | 0.25427 | 0.25427 | 0.20585 | 0.20585 | 0.20585 |
| process[Recruitment].ycs_values{2004} | 0.20174 | 0.20174 | 0.20174 | 0.25238 | 0.25238 | 0.20174 | 0.20174 | 0.20174 |
| process[Recruitment].ycs_values{2005} | 0.25678 | 0.25678 | 0.25678 | 0.32495 | 0.32495 | 0.25678 | 0.25678 | 0.25678 |
| process[Recruitment].ycs_values{2006} | 1.31409 | 1.31409 | 1.31409 | 1.69567 | 1.69567 | 1.31409 | 1.31409 | 1.31409 |
| process[Recruitment].ycs_values{2007} | 0.52328 | 0.52328 | 0.52328 | 0.68660 | 0.68660 | 0.52328 | 0.52328 | 0.52328 |
| process[Recruitment].ycs_values{2008} | 0.15242 | 0.15242 | 0.15242 | 0.20067 | 0.20067 | 0.15242 | 0.15242 | 0.15242 |
| process[Recruitment].ycs_values{2009} | 0.87606 | 0.87606 | 0.87606 | 1.20372 | 1.20372 | 0.87606 | 0.87606 | 0.87606 |
| process[Recruitment].ycs_values{2010} | 0.00772 | 0.00772 | 0.00772 | 0.16935 | 0.16935 | 0.00772 | 0.00772 | 0.00772 |
| process[Recruitment].ycs_values{2011} | 0.59070 | 0.59070 | 0.59070 | 0.87569 | 0.87569 | 0.59070 | 0.59070 | 0.59070 |
| process[Recruitment].ycs_values{2012} | 0.09495 | 0.09495 | 0.09495 | 0.13266 | 0.13266 | 0.09495 | 0.09495 | 0.09495 |
| process[Instantaneous_Mortality].m{male.nonspawn} | 0.15745 | 0.15745 | 0.15745 | 0.15118 | 0.15118 | 0.15745 | 0.15745 | 0.15745 |
| process[Instantaneous_Mortality].m{female.nonspawn} | 0.16651 | 0.16651 | 0.16651 | 0.16033 | 0.16033 | 0.16651 | 0.16651 | 0.16651 |
| observation[TangaroaAcousticMature].process_error | 0.00010 | 0.00010 | 0.00010 | 0.00010 | 0.00010 | 0.00010 | 0.00010 | 0.00010 |
| rownames | betadiff_casal_flags_on | betadiff_casal_flags_off | betadiff_casal_flags_on_low_tol | cppad_casal_flags_on | cppad_casal_flags_off | adolc_casal_flags_on | adolc_casal_flags_off | adolc_casal_flags_on_low_tol |
|---|---|---|---|---|---|---|---|---|
| process[Recruitment].b0 | 0.000 | 0.000 | 0.000 | -4.979 | -4.979 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_male].v{1} | 0.000 | 0.000 | 0.000 | -0.254 | -0.254 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_male].v{2} | 0.000 | 0.000 | 0.000 | 0.725 | 0.725 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_male].v{3} | 0.000 | 0.000 | 0.000 | 0.321 | 0.321 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_male].v{4} | 0.000 | 0.000 | 0.000 | -12.654 | -12.654 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_female].v{1} | 0.000 | 0.000 | 0.000 | -0.211 | -0.211 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_female].v{2} | 0.000 | 0.000 | 0.000 | 0.601 | 0.601 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_female].v{3} | 0.000 | 0.000 | 0.000 | 0.484 | 0.484 | 0.000 | 0.000 | 0.000 |
| selectivity[MaturationSel_female].v{4} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1958} | 0.000 | 0.000 | 0.000 | -1.673 | -1.673 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1959} | 0.000 | 0.000 | 0.000 | -1.847 | -1.847 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1960} | 0.000 | 0.000 | 0.000 | -2.036 | -2.036 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1961} | 0.000 | 0.000 | 0.000 | -2.242 | -2.242 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1962} | 0.000 | 0.000 | 0.000 | -2.479 | -2.479 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1963} | 0.000 | 0.000 | 0.000 | -2.703 | -2.703 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1964} | 0.000 | 0.000 | 0.000 | -2.902 | -2.902 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1965} | 0.000 | 0.000 | 0.000 | -16.643 | -16.643 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1966} | 0.000 | 0.000 | 0.000 | -14.570 | -14.570 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1967} | 0.000 | 0.000 | 0.000 | -14.993 | -14.993 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1968} | 0.000 | 0.000 | 0.000 | -15.121 | -15.121 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1969} | 0.000 | 0.000 | 0.000 | -14.081 | -14.081 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1970} | 0.000 | 0.000 | 0.000 | -13.297 | -13.297 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1971} | 0.000 | 0.000 | 0.000 | -16.229 | -16.229 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1972} | 0.000 | 0.000 | 0.000 | -16.169 | -16.169 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1973} | 0.000 | 0.000 | 0.000 | -15.536 | -15.536 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1974} | 0.000 | 0.000 | 0.000 | -16.571 | -16.571 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1975} | 0.000 | 0.000 | 0.000 | -18.367 | -18.367 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1976} | 0.000 | 0.000 | 0.000 | -17.388 | -17.388 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1977} | 0.000 | 0.000 | 0.000 | -17.382 | -17.382 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1978} | 0.000 | 0.000 | 0.000 | -18.215 | -18.215 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1979} | 0.000 | 0.000 | 0.000 | -20.174 | -20.174 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1980} | 0.000 | 0.000 | 0.000 | -20.787 | -20.787 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1981} | 0.000 | 0.000 | 0.000 | -20.557 | -20.557 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1982} | 0.000 | 0.000 | 0.000 | -19.235 | -19.235 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1983} | 0.000 | 0.000 | 0.000 | -21.335 | -21.335 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1984} | 0.000 | 0.000 | 0.000 | -21.601 | -21.601 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1985} | 0.000 | 0.000 | 0.000 | -21.613 | -21.613 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1986} | 0.000 | 0.000 | 0.000 | -21.907 | -21.907 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1987} | 0.000 | 0.000 | 0.000 | -21.632 | -21.632 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1988} | 0.000 | 0.000 | 0.000 | -22.100 | -22.100 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1989} | 0.000 | 0.000 | 0.000 | -19.633 | -19.633 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1990} | 0.000 | 0.000 | 0.000 | -21.217 | -21.217 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1991} | 0.000 | 0.000 | 0.000 | -21.270 | -21.270 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1992} | 0.000 | 0.000 | 0.000 | -21.350 | -21.350 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1993} | 0.000 | 0.000 | 0.000 | -20.955 | -20.955 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1994} | 0.000 | 0.000 | 0.000 | -19.208 | -19.208 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1995} | 0.000 | 0.000 | 0.000 | -21.162 | -21.162 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1996} | 0.000 | 0.000 | 0.000 | -20.809 | -20.809 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1997} | 0.000 | 0.000 | 0.000 | -19.754 | -19.754 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1998} | 0.000 | 0.000 | 0.000 | -21.087 | -21.087 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{1999} | 0.000 | 0.000 | 0.000 | -20.132 | -20.132 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2000} | 0.000 | 0.000 | 0.000 | -21.324 | -21.324 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2001} | 0.000 | 0.000 | 0.000 | -22.645 | -22.645 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2002} | 0.000 | 0.000 | 0.000 | -23.517 | -23.517 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2003} | 0.000 | 0.000 | 0.000 | -23.521 | -23.521 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2004} | 0.000 | 0.000 | 0.000 | -25.098 | -25.098 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2005} | 0.000 | 0.000 | 0.000 | -26.551 | -26.551 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2006} | 0.000 | 0.000 | 0.000 | -29.038 | -29.038 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2007} | 0.000 | 0.000 | 0.000 | -31.210 | -31.210 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2008} | 0.000 | 0.000 | 0.000 | -31.658 | -31.658 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2009} | 0.000 | 0.000 | 0.000 | -37.401 | -37.401 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2010} | 0.000 | 0.000 | 0.000 | -2093.890 | -2093.890 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2011} | 0.000 | 0.000 | 0.000 | -48.246 | -48.246 | 0.000 | 0.000 | 0.000 |
| process[Recruitment].ycs_values{2012} | 0.000 | 0.000 | 0.000 | -39.718 | -39.718 | 0.000 | 0.000 | 0.000 |
| process[Instantaneous_Mortality].m{male.nonspawn} | 0.000 | 0.000 | 0.000 | 3.978 | 3.978 | 0.000 | 0.000 | 0.000 |
| process[Instantaneous_Mortality].m{female.nonspawn} | 0.000 | 0.000 | 0.000 | 3.713 | 3.713 | 0.000 | 0.000 | 0.000 |
| observation[TangaroaAcousticMature].process_error | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| Component | Base_Model | Sensitivity_1 |
|---|---|---|
| TangaroaAcousticImmature | 17.980 | 17.980 |
| TangaroaAcousticMature | -9.196 | -9.196 |
| ObserverProportionsAtAge | 957.800 | 957.800 |
| prior_on_initialization.B0 | 12.660 | 12.660 |
| prior_on_relative_abundance[TangaroaAcousticMature].cv_process_error | -9.210 | -9.210 |
| prior_on_natural_mortality.avg | -1.183 | -1.183 |
| prior_on_natural_mortality.diff | 0.017 | 0.017 |
| prior_on_migration[toSpawn].rates_male | 0.000 | 0.000 |
| prior_on_migration[toSpawn].rates_female | 0.000 | 0.000 |
| prior_on_recruitment.YCS | -30.170 | -30.170 |
| prior_on_q_TangaroaImmatureq | 0.000 | 0.000 |
| prior_on_q_TangaroaMatureq | -0.732 | -0.732 |
| Penalty-CatchLimitTrawl | 0.000 | 0.000 |
| Penalty-YCS | 0.397 | 0.397 |
| Total | 938.400 | 938.400 |
| rownames | betadiff_casal_flags_on | betadiff_casal_flags_off | betadiff_casal_flags_on_low_tol | cppad_casal_flags_on | cppad_casal_flags_off | adolc_casal_flags_on | adolc_casal_flags_off | adolc_casal_flags_on_low_tol |
|---|---|---|---|---|---|---|---|---|
| observation->TangaroaAcousticMature-1993 | -1.281 | -1.281 | -1.281 | -1.371 | -1.371 | -1.281 | -1.281 | -1.281 |
| observation->TangaroaAcousticMature-1994 | -0.601 | -0.601 | -0.601 | -0.439 | -0.439 | -0.601 | -0.601 | -0.601 |
| observation->TangaroaAcousticMature-1995 | -0.448 | -0.448 | -0.448 | -0.622 | -0.622 | -0.448 | -0.448 | -0.448 |
| observation->TangaroaAcousticMature-1998 | -1.707 | -1.707 | -1.707 | -1.531 | -1.531 | -1.707 | -1.707 | -1.707 |
| observation->TangaroaAcousticMature-2000 | -1.778 | -1.778 | -1.778 | -1.764 | -1.764 | -1.778 | -1.778 | -1.778 |
| observation->TangaroaAcousticMature-2002 | -0.369 | -0.369 | -0.369 | -0.358 | -0.358 | -0.369 | -0.369 | -0.369 |
| observation->TangaroaAcousticMature-2004 | -0.784 | -0.784 | -0.784 | -0.807 | -0.807 | -0.784 | -0.784 | -0.784 |
| observation->TangaroaAcousticMature-2006 | -0.888 | -0.888 | -0.888 | -0.881 | -0.881 | -0.888 | -0.888 | -0.888 |
| observation->TangaroaAcousticMature-2009 | 0.699 | 0.699 | 0.699 | 0.455 | 0.455 | 0.699 | 0.699 | 0.699 |
| observation->TangaroaAcousticMature-2011 | -1.004 | -1.004 | -1.004 | -0.638 | -0.638 | -1.004 | -1.004 | -1.004 |
| observation->TangaroaAcousticMature-2013 | -1.401 | -1.401 | -1.401 | -1.239 | -1.239 | -1.401 | -1.401 | -1.401 |
| observation->TangaroaAcousticImmature-1993 | 1.968 | 1.968 | 1.968 | 2.542 | 2.542 | 1.968 | 1.968 | 1.968 |
| observation->TangaroaAcousticImmature-1994 | 0.817 | 0.817 | 0.817 | 0.618 | 0.618 | 0.817 | 0.817 | 0.817 |
| observation->TangaroaAcousticImmature-1995 | 1.945 | 1.945 | 1.945 | 2.199 | 2.199 | 1.945 | 1.945 | 1.945 |
| observation->TangaroaAcousticImmature-1998 | -1.536 | -1.536 | -1.536 | -1.444 | -1.444 | -1.536 | -1.536 | -1.536 |
| observation->TangaroaAcousticImmature-2000 | 4.866 | 4.866 | 4.866 | 4.306 | 4.306 | 4.866 | 4.866 | 4.866 |
| observation->TangaroaAcousticImmature-2002 | 7.321 | 7.321 | 7.321 | 7.122 | 7.122 | 7.321 | 7.321 | 7.321 |
| observation->TangaroaAcousticImmature-2004 | 1.722 | 1.722 | 1.722 | 1.430 | 1.430 | 1.722 | 1.722 | 1.722 |
| observation->TangaroaAcousticImmature-2006 | -0.467 | -0.467 | -0.467 | -0.524 | -0.524 | -0.467 | -0.467 | -0.467 |
| observation->TangaroaAcousticImmature-2009 | 2.221 | 2.221 | 2.221 | 1.845 | 1.845 | 2.221 | 2.221 | 2.221 |
| observation->TangaroaAcousticImmature-2011 | 1.543 | 1.543 | 1.543 | 0.514 | 0.514 | 1.543 | 1.543 | 1.543 |
| observation->TangaroaAcousticImmature-2013 | -0.388 | -0.388 | -0.388 | -0.628 | -0.628 | -0.388 | -0.388 | -0.388 |
| observation->ObserverProportionsAtAge-1979 | 15.198 | 15.198 | 15.198 | 15.170 | 15.170 | 15.198 | 15.198 | 15.198 |
| observation->ObserverProportionsAtAge-1980 | 17.076 | 17.076 | 17.076 | 16.997 | 16.997 | 17.076 | 17.076 | 17.076 |
| observation->ObserverProportionsAtAge-1981 | 30.961 | 30.961 | 30.961 | 30.816 | 30.816 | 30.961 | 30.961 | 30.961 |
| observation->ObserverProportionsAtAge-1982 | 26.030 | 26.030 | 26.030 | 25.988 | 25.988 | 26.030 | 26.030 | 26.030 |
| observation->ObserverProportionsAtAge-1983 | 20.423 | 20.423 | 20.423 | 20.405 | 20.405 | 20.423 | 20.423 | 20.423 |
| observation->ObserverProportionsAtAge-1984 | 26.174 | 26.174 | 26.174 | 26.188 | 26.188 | 26.174 | 26.174 | 26.174 |
| observation->ObserverProportionsAtAge-1985 | 22.917 | 22.917 | 22.917 | 22.925 | 22.925 | 22.917 | 22.917 | 22.917 |
| observation->ObserverProportionsAtAge-1986 | 27.628 | 27.628 | 27.628 | 27.666 | 27.666 | 27.628 | 27.628 | 27.628 |
| observation->ObserverProportionsAtAge-1987 | 28.825 | 28.825 | 28.825 | 28.852 | 28.852 | 28.825 | 28.825 | 28.825 |
| observation->ObserverProportionsAtAge-1988 | 28.862 | 28.862 | 28.862 | 28.852 | 28.852 | 28.862 | 28.862 | 28.862 |
| observation->ObserverProportionsAtAge-1989 | 31.713 | 31.713 | 31.713 | 31.664 | 31.664 | 31.713 | 31.713 | 31.713 |
| observation->ObserverProportionsAtAge-1990 | 28.187 | 28.187 | 28.187 | 28.167 | 28.167 | 28.187 | 28.187 | 28.187 |
| observation->ObserverProportionsAtAge-1991 | 37.659 | 37.659 | 37.659 | 37.701 | 37.701 | 37.659 | 37.659 | 37.659 |
| observation->ObserverProportionsAtAge-1992 | 28.026 | 28.026 | 28.026 | 28.005 | 28.005 | 28.026 | 28.026 | 28.026 |
| observation->ObserverProportionsAtAge-1993 | 29.232 | 29.232 | 29.232 | 29.218 | 29.218 | 29.232 | 29.232 | 29.232 |
| observation->ObserverProportionsAtAge-1994 | 22.142 | 22.142 | 22.142 | 22.182 | 22.182 | 22.142 | 22.142 | 22.142 |
| observation->ObserverProportionsAtAge-1995 | 21.909 | 21.909 | 21.909 | 21.880 | 21.880 | 21.909 | 21.909 | 21.909 |
| observation->ObserverProportionsAtAge-1996 | 25.898 | 25.898 | 25.898 | 25.957 | 25.957 | 25.898 | 25.898 | 25.898 |
| observation->ObserverProportionsAtAge-1997 | 21.104 | 21.104 | 21.104 | 21.121 | 21.121 | 21.104 | 21.104 | 21.104 |
| observation->ObserverProportionsAtAge-1998 | 20.384 | 20.384 | 20.384 | 20.366 | 20.366 | 20.384 | 20.384 | 20.384 |
| observation->ObserverProportionsAtAge-1999 | 24.422 | 24.422 | 24.422 | 24.462 | 24.462 | 24.422 | 24.422 | 24.422 |
| observation->ObserverProportionsAtAge-2000 | 16.719 | 16.719 | 16.719 | 16.759 | 16.759 | 16.719 | 16.719 | 16.719 |
| observation->ObserverProportionsAtAge-2001 | 26.268 | 26.268 | 26.268 | 26.422 | 26.422 | 26.268 | 26.268 | 26.268 |
| observation->ObserverProportionsAtAge-2002 | 20.049 | 20.049 | 20.049 | 20.058 | 20.058 | 20.049 | 20.049 | 20.049 |
| observation->ObserverProportionsAtAge-2003 | 34.053 | 34.053 | 34.053 | 33.941 | 33.941 | 34.053 | 34.053 | 34.053 |
| observation->ObserverProportionsAtAge-2004 | 18.376 | 18.376 | 18.376 | 18.369 | 18.369 | 18.376 | 18.376 | 18.376 |
| observation->ObserverProportionsAtAge-2005 | 27.993 | 27.993 | 27.993 | 28.123 | 28.123 | 27.993 | 27.993 | 27.993 |
| observation->ObserverProportionsAtAge-2006 | 23.330 | 23.330 | 23.330 | 23.299 | 23.299 | 23.330 | 23.330 | 23.330 |
| observation->ObserverProportionsAtAge-2007 | 26.652 | 26.652 | 26.652 | 26.685 | 26.685 | 26.652 | 26.652 | 26.652 |
| observation->ObserverProportionsAtAge-2008 | 37.886 | 37.886 | 37.886 | 37.858 | 37.858 | 37.886 | 37.886 | 37.886 |
| observation->ObserverProportionsAtAge-2009 | 20.404 | 20.404 | 20.404 | 20.375 | 20.375 | 20.404 | 20.404 | 20.404 |
| observation->ObserverProportionsAtAge-2010 | 27.646 | 27.646 | 27.646 | 27.660 | 27.660 | 27.646 | 27.646 | 27.646 |
| observation->ObserverProportionsAtAge-2011 | 25.050 | 25.050 | 25.050 | 25.087 | 25.087 | 25.050 | 25.050 | 25.050 |
| observation->ObserverProportionsAtAge-2012 | 27.283 | 27.283 | 27.283 | 26.836 | 26.836 | 27.283 | 27.283 | 27.283 |
| observation->ObserverProportionsAtAge-2013 | 25.155 | 25.155 | 25.155 | 27.976 | 27.976 | 25.155 | 25.155 | 25.155 |
| observation->ObserverProportionsAtAge-2014 | 49.117 | 49.117 | 49.117 | 35.395 | 35.395 | 49.117 | 49.117 | 49.117 |
| observation->ObserverProportionsAtAge-2015 | 34.203 | 34.203 | 34.203 | 28.362 | 28.362 | 34.203 | 34.203 | 34.203 |
| prior->B0->process[Recruitment].b0 | 12.610 | 12.610 | 12.610 | 12.659 | 12.659 | 12.610 | 12.610 | 12.610 |
| prior->Migration_male->selectivity[MaturationSel_male].v{1} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_male->selectivity[MaturationSel_male].v{2} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_male->selectivity[MaturationSel_male].v{3} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_male->selectivity[MaturationSel_male].v{4} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_female->selectivity[MaturationSel_female].v{1} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_female->selectivity[MaturationSel_female].v{2} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_female->selectivity[MaturationSel_female].v{3} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->Migration_female->selectivity[MaturationSel_female].v{4} | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| prior->YCS->process[Recruitment].ycs_values{1958} | -0.984 | -0.984 | -0.984 | -0.982 | -0.982 | -0.984 | -0.984 | -0.984 |
| prior->YCS->process[Recruitment].ycs_values{1959} | -0.982 | -0.982 | -0.982 | -0.979 | -0.979 | -0.982 | -0.982 | -0.982 |
| prior->YCS->process[Recruitment].ycs_values{1960} | -0.979 | -0.979 | -0.979 | -0.976 | -0.976 | -0.979 | -0.979 | -0.979 |
| prior->YCS->process[Recruitment].ycs_values{1961} | -0.975 | -0.975 | -0.975 | -0.971 | -0.971 | -0.975 | -0.975 | -0.975 |
| prior->YCS->process[Recruitment].ycs_values{1962} | -0.970 | -0.970 | -0.970 | -0.965 | -0.965 | -0.970 | -0.970 | -0.970 |
| prior->YCS->process[Recruitment].ycs_values{1963} | -0.962 | -0.962 | -0.962 | -0.955 | -0.955 | -0.962 | -0.962 | -0.962 |
| prior->YCS->process[Recruitment].ycs_values{1964} | -0.950 | -0.950 | -0.950 | -0.941 | -0.941 | -0.950 | -0.950 | -0.950 |
| prior->YCS->process[Recruitment].ycs_values{1965} | -0.336 | -0.336 | -0.336 | -0.147 | -0.147 | -0.336 | -0.336 | -0.336 |
| prior->YCS->process[Recruitment].ycs_values{1966} | -0.730 | -0.730 | -0.730 | -0.622 | -0.622 | -0.730 | -0.730 | -0.730 |
| prior->YCS->process[Recruitment].ycs_values{1967} | -0.927 | -0.927 | -0.927 | -0.867 | -0.867 | -0.927 | -0.927 | -0.927 |
| prior->YCS->process[Recruitment].ycs_values{1968} | -0.989 | -0.989 | -0.989 | -0.976 | -0.976 | -0.989 | -0.989 | -0.989 |
| prior->YCS->process[Recruitment].ycs_values{1969} | -0.793 | -0.793 | -0.793 | -0.867 | -0.867 | -0.793 | -0.793 | -0.793 |
| prior->YCS->process[Recruitment].ycs_values{1970} | -0.306 | -0.306 | -0.306 | -0.445 | -0.445 | -0.306 | -0.306 | -0.306 |
| prior->YCS->process[Recruitment].ycs_values{1971} | -0.858 | -0.858 | -0.858 | -0.924 | -0.924 | -0.858 | -0.858 | -0.858 |
| prior->YCS->process[Recruitment].ycs_values{1972} | -0.574 | -0.574 | -0.574 | -0.700 | -0.700 | -0.574 | -0.574 | -0.574 |
| prior->YCS->process[Recruitment].ycs_values{1973} | 0.170 | 0.170 | 0.170 | -0.041 | -0.041 | 0.170 | 0.170 | 0.170 |
| prior->YCS->process[Recruitment].ycs_values{1974} | 0.101 | 0.101 | 0.101 | -0.115 | -0.115 | 0.101 | 0.101 | 0.101 |
| prior->YCS->process[Recruitment].ycs_values{1975} | -0.708 | -0.708 | -0.708 | -0.821 | -0.821 | -0.708 | -0.708 | -0.708 |
| prior->YCS->process[Recruitment].ycs_values{1976} | 0.404 | 0.404 | 0.404 | 0.148 | 0.148 | 0.404 | 0.404 | 0.404 |
| prior->YCS->process[Recruitment].ycs_values{1977} | 0.844 | 0.844 | 0.844 | 0.549 | 0.549 | 0.844 | 0.844 | 0.844 |
| prior->YCS->process[Recruitment].ycs_values{1978} | 0.436 | 0.436 | 0.436 | 0.166 | 0.166 | 0.436 | 0.436 | 0.436 |
| prior->YCS->process[Recruitment].ycs_values{1979} | -0.937 | -0.937 | -0.937 | -0.860 | -0.860 | -0.937 | -0.937 | -0.937 |
| prior->YCS->process[Recruitment].ycs_values{1980} | -0.945 | -0.945 | -0.945 | -0.871 | -0.871 | -0.945 | -0.945 | -0.945 |
| prior->YCS->process[Recruitment].ycs_values{1981} | -0.414 | -0.414 | -0.414 | -0.598 | -0.598 | -0.414 | -0.414 | -0.414 |
| prior->YCS->process[Recruitment].ycs_values{1982} | 1.258 | 1.258 | 1.258 | 0.898 | 0.898 | 1.258 | 1.258 | 1.258 |
| prior->YCS->process[Recruitment].ycs_values{1983} | -0.741 | -0.741 | -0.741 | -0.859 | -0.859 | -0.741 | -0.741 | -0.741 |
| prior->YCS->process[Recruitment].ycs_values{1984} | -0.709 | -0.709 | -0.709 | -0.837 | -0.837 | -0.709 | -0.709 | -0.709 |
| prior->YCS->process[Recruitment].ycs_values{1985} | -0.584 | -0.584 | -0.584 | -0.742 | -0.742 | -0.584 | -0.584 | -0.584 |
| prior->YCS->process[Recruitment].ycs_values{1986} | -0.989 | -0.989 | -0.989 | -0.962 | -0.962 | -0.989 | -0.989 | -0.989 |
| prior->YCS->process[Recruitment].ycs_values{1987} | -0.692 | -0.692 | -0.692 | -0.824 | -0.824 | -0.692 | -0.692 | -0.692 |
| prior->YCS->process[Recruitment].ycs_values{1988} | -0.883 | -0.883 | -0.883 | -0.771 | -0.771 | -0.883 | -0.883 | -0.883 |
| prior->YCS->process[Recruitment].ycs_values{1989} | 1.076 | 1.076 | 1.076 | 0.726 | 0.726 | 1.076 | 1.076 | 1.076 |
| prior->YCS->process[Recruitment].ycs_values{1990} | -0.987 | -0.987 | -0.987 | -0.982 | -0.982 | -0.987 | -0.987 | -0.987 |
| prior->YCS->process[Recruitment].ycs_values{1991} | 1.692 | 1.692 | 1.692 | 2.159 | 2.159 | 1.692 | 1.692 | 1.692 |
| prior->YCS->process[Recruitment].ycs_values{1992} | -0.736 | -0.736 | -0.736 | -0.578 | -0.578 | -0.736 | -0.736 | -0.736 |
| prior->YCS->process[Recruitment].ycs_values{1993} | -0.989 | -0.989 | -0.989 | -0.978 | -0.978 | -0.989 | -0.989 | -0.989 |
| prior->YCS->process[Recruitment].ycs_values{1994} | -0.700 | -0.700 | -0.700 | -0.819 | -0.819 | -0.700 | -0.700 | -0.700 |
| prior->YCS->process[Recruitment].ycs_values{1995} | -0.733 | -0.733 | -0.733 | -0.576 | -0.576 | -0.733 | -0.733 | -0.733 |
| prior->YCS->process[Recruitment].ycs_values{1996} | -0.950 | -0.950 | -0.950 | -0.879 | -0.879 | -0.950 | -0.950 | -0.950 |
| prior->YCS->process[Recruitment].ycs_values{1997} | -0.790 | -0.790 | -0.790 | -0.888 | -0.888 | -0.790 | -0.790 | -0.790 |
| prior->YCS->process[Recruitment].ycs_values{1998} | -0.977 | -0.977 | -0.977 | -0.929 | -0.929 | -0.977 | -0.977 | -0.977 |
| prior->YCS->process[Recruitment].ycs_values{1999} | -0.929 | -0.929 | -0.929 | -0.976 | -0.976 | -0.929 | -0.929 | -0.929 |
| prior->YCS->process[Recruitment].ycs_values{2000} | -0.986 | -0.986 | -0.986 | -0.951 | -0.951 | -0.986 | -0.986 | -0.986 |
| prior->YCS->process[Recruitment].ycs_values{2001} | -0.552 | -0.552 | -0.552 | -0.339 | -0.339 | -0.552 | -0.552 | -0.552 |
| prior->YCS->process[Recruitment].ycs_values{2002} | -0.909 | -0.909 | -0.909 | -0.801 | -0.801 | -0.909 | -0.909 | -0.909 |
| prior->YCS->process[Recruitment].ycs_values{2003} | -0.985 | -0.985 | -0.985 | -0.983 | -0.983 | -0.985 | -0.985 | -0.985 |
| prior->YCS->process[Recruitment].ycs_values{2004} | -0.983 | -0.983 | -0.983 | -0.984 | -0.984 | -0.983 | -0.983 | -0.983 |
| prior->YCS->process[Recruitment].ycs_values{2005} | -0.982 | -0.982 | -0.982 | -0.924 | -0.924 | -0.982 | -0.982 | -0.982 |
| prior->YCS->process[Recruitment].ycs_values{2006} | 0.571 | 0.571 | 0.571 | 1.057 | 1.057 | 0.571 | 0.571 | 0.571 |
| prior->YCS->process[Recruitment].ycs_values{2007} | -0.636 | -0.636 | -0.636 | -0.369 | -0.369 | -0.636 | -0.636 | -0.636 |
| prior->YCS->process[Recruitment].ycs_values{2008} | -0.910 | -0.910 | -0.910 | -0.982 | -0.982 | -0.910 | -0.910 | -0.910 |
| prior->YCS->process[Recruitment].ycs_values{2009} | -0.066 | -0.066 | -0.066 | 0.419 | 0.419 | -0.066 | -0.066 | -0.066 |
| prior->YCS->process[Recruitment].ycs_values{2010} | 4.782 | 4.782 | 4.782 | -0.947 | -0.947 | 4.782 | 4.782 | 4.782 |
| prior->YCS->process[Recruitment].ycs_values{2011} | -0.526 | -0.526 | -0.526 | -0.067 | -0.067 | -0.526 | -0.526 | -0.526 |
| prior->YCS->process[Recruitment].ycs_values{2012} | -0.607 | -0.607 | -0.607 | -0.845 | -0.845 | -0.607 | -0.607 | -0.607 |
| prior->M_male_with_avg_prior->process[Instantaneous_Mortality].m{male.nonspawn} | -1.354 | -1.354 | -1.354 | -1.183 | -1.183 | -1.354 | -1.354 | -1.354 |
| prior->M_female_with_diff_prior->process[Instantaneous_Mortality].m{female.nonspawn} | 0.016 | 0.016 | 0.016 | 0.017 | 0.017 | 0.016 | 0.016 | 0.016 |
| prior->mature_process_error->observation[TangaroaAcousticMature].process_error | -9.210 | -9.210 | -9.210 | -9.210 | -9.210 | -9.210 | -9.210 | -9.210 |
| additional_prior->Penalty-YCS | 0.483 | 0.483 | 0.483 | 0.397 | 0.397 | 0.483 | 0.483 | 0.483 |
| additional_prior->TangaroaMatureq | -0.713 | -0.713 | -0.713 | -0.732 | -0.732 | -0.713 | -0.713 | -0.713 |
| jacobian->avg_diff | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 | 0.000 |
| total_negloglike | 962.721 | 962.721 | 962.721 | 938.228 | 938.228 | 962.721 | 962.721 | 962.721 |
## [1] "CASAL base model convergence information"
## [1] "Minimiser convergence threshold: 2e-006"
## [2] "fmm: have converged: t = 1.56689e-006 f = 938.352"
## [3] "Successful convergence in optimise"
## [4] "Minimiser achieved convergence after 260 quasi-Newton iterations using 321 objective function evaluations"
## [1] ""
## [1] "CASAL sensitivity 1 model convergence information"
## [1] "Minimiser convergence threshold: 1e-009"
## [2] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [3] "Successful convergence in optimise"
## [4] "Minimiser achieved convergence after 270 quasi-Newton iterations using 338 objective function evaluations"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model convergence information"
## [1] "fmm: have converged: t = 1.7148e-07 f = 973.615"
## [2] "Successful convergence in optimise"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model convergence information"
## [1] "fmm: have converged: t = 1.40909e-07 f = 973.615"
## [2] "Successful convergence in optimise"
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model convergence information"
## [1] "fmm: step size too small. Indicates successful convergence (though this is not the textbook ideal convergence situation)"
## [2] "Successful convergence in optimise"
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model convergence information"
## [1] "Number of nonzeros in equality constraint Jacobian...: 0"
## [2] "Number of nonzeros in inequality constraint Jacobian.: 67"
## [3] "Number of nonzeros in Lagrangian Hessian.............: 2278"
## [4] "Number of Iterations....: 66"
## [5] "Number of objective function evaluations = 89"
## [6] "Number of objective gradient evaluations = 67"
## [7] "Number of equality constraint evaluations = 0"
## [8] "Number of inequality constraint evaluations = 89"
## [9] "Number of equality constraint Jacobian evaluations = 0"
## [10] "Number of inequality constraint Jacobian evaluations = 67"
## [11] "Number of Lagrangian Hessian evaluations = 66"
## [12] "EXIT: Optimal Solution Found."
## [13] "Number of nonzeros in equality constraint Jacobian...: 0"
## [14] "Number of nonzeros in inequality constraint Jacobian.: 67"
## [15] "Number of nonzeros in Lagrangian Hessian.............: 2278"
## [16] "Number of Iterations....: 29"
## [17] "Number of objective function evaluations = 44"
## [18] "Number of objective gradient evaluations = 30"
## [19] "Number of equality constraint evaluations = 0"
## [20] "Number of inequality constraint evaluations = 44"
## [21] "Number of equality constraint Jacobian evaluations = 0"
## [22] "Number of inequality constraint Jacobian evaluations = 30"
## [23] "Number of Lagrangian Hessian evaluations = 29"
## [24] "EXIT: Optimal Solution Found."
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model convergence information"
## [1] "Number of nonzeros in equality constraint Jacobian...: 0"
## [2] "Number of nonzeros in inequality constraint Jacobian.: 67"
## [3] "Number of nonzeros in Lagrangian Hessian.............: 2278"
## [4] "Number of Iterations....: 66"
## [5] "Number of objective function evaluations = 89"
## [6] "Number of objective gradient evaluations = 67"
## [7] "Number of equality constraint evaluations = 0"
## [8] "Number of inequality constraint evaluations = 89"
## [9] "Number of equality constraint Jacobian evaluations = 0"
## [10] "Number of inequality constraint Jacobian evaluations = 67"
## [11] "Number of Lagrangian Hessian evaluations = 66"
## [12] "EXIT: Optimal Solution Found."
## [13] "Number of nonzeros in equality constraint Jacobian...: 0"
## [14] "Number of nonzeros in inequality constraint Jacobian.: 67"
## [15] "Number of nonzeros in Lagrangian Hessian.............: 2278"
## [16] "Number of Iterations....: 29"
## [17] "Number of objective function evaluations = 44"
## [18] "Number of objective gradient evaluations = 30"
## [19] "Number of equality constraint evaluations = 0"
## [20] "Number of inequality constraint evaluations = 44"
## [21] "Number of equality constraint Jacobian evaluations = 0"
## [22] "Number of inequality constraint Jacobian evaluations = 30"
## [23] "Number of Lagrangian Hessian evaluations = 29"
## [24] "EXIT: Optimal Solution Found."
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model convergence information"
## character(0)
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model convergence information"
## character(0)
## [1] "CASAL model warnings"
## parameter estimate
## 1 relative_abundance[TangaroaAcousticMature].cv_process_error 0.0001
## 2 migration[toSpawn].rates_female[4] 0.999
## 3 recruitment.YCS[13] 0.08025
## 4 recruitment.YCS[16] 0.05757
## 5 recruitment.YCS[17] 0.06079
## 6 recruitment.YCS[19] 0.05057
## 7 recruitment.YCS[20] 0.03959
## 8 recruitment.YCS[21] 0.04996
## 9 recruitment.YCS[24] 0.09402
## 10 recruitment.YCS[25] 0.0328
## 11 recruitment.YCS[32] 0.0359
## lower.bound upper.bound
## 1 0.0001 1
## 2 0.001 0.999
## 3 0.001 100
## 4 0.001 100
## 5 0.001 100
## 6 0.001 100
## 7 0.001 100
## 8 0.001 100
## 9 0.001 100
## 10 0.001 100
## 11 0.001 100
## [1] ""
## [1] "CASAL sensitivity 1 model warnings"
## parameter estimate
## 1 relative_abundance[TangaroaAcousticMature].cv_process_error 0.0001
## 2 migration[toSpawn].rates_female[4] 0.999
## 3 recruitment.YCS[13] 0.08025
## 4 recruitment.YCS[16] 0.05757
## 5 recruitment.YCS[17] 0.06079
## 6 recruitment.YCS[19] 0.05057
## 7 recruitment.YCS[20] 0.03959
## 8 recruitment.YCS[21] 0.04996
## 9 recruitment.YCS[24] 0.09402
## 10 recruitment.YCS[25] 0.0328
## 11 recruitment.YCS[32] 0.0359
## lower.bound upper.bound
## 1 0.0001 1
## 2 0.001 0.999
## 3 0.001 100
## 4 0.001 100
## 5 0.001 100
## 6 0.001 100
## 7 0.001 100
## 8 0.001 100
## 9 0.001 100
## 10 0.001 100
## 11 0.001 100
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 betadiff_casal_flags_off model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 betadiff_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 cppad_casal_flags_on model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 cppad_casal_flags_off model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 adolc_casal_flags_on model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 adolc_casal_flags_off model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
##
## [1] ""
## [1] "Casal2 adolc_casal_flags_on_low_tol model warnings"
## $warnings_found
## [1] 4
##
## $warning_0
## [1] "Estimates were removed because of matching lower and upper bounds. Originally had 69 estimates, now have 67"
##
## $warning_1
## [1] "estimated parameter 'selectivity[MaturationSel_female].v{4}' was within 0.001 of upper bound 0.999"
##
## $warning_2
## [1] "estimated parameter 'process[Instantaneous_Mortality].m{female.nonspawn}' was within 0.001 of upper bound 0.05"
##
## $warning_3
## [1] "estimated parameter 'observation[TangaroaAcousticMature].process_error' was within 0.001 of lower bound 0.0001"
##
## $type
## [1] "warnings"
Time series comparisons with CASAL base model results
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run betadiff_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run cppad_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_off"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
## [1] "Catch time series base model comparison for run adolc_casal_flags_on_low_tol"
## [1] "Actual catches for Trawl match: yes"
## [1] ""
Derived quantities
SB0, SBcurrent, MSY, F_MSY, others...
Comparison plots
## [1] "CASAL base parameter correlation range (excluding 1.0): -0.5771 0.7601"
## [1] "CASAL sensitivity 1 parameter correlation range (excluding 1.0): -0.465 0.7616"
## Warning in min(x): no non-missing arguments to min; returning Inf
## Warning in max(x): no non-missing arguments to max; returning -Inf
## [1] "Casal2 betadiff_casal_flags_on parameter correlation range (excluding 1.0): Inf -Inf"
## [1] "Casal2 betadiff_casal_flags_off parameter correlation range (excluding 1.0): -0.474750601346601 0.754913095502236"
## [1] "Casal2 betadiff_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.828728281162341 0.771401949199379"
## [1] "Casal2 cppad_casal_flags_on parameter correlation range (excluding 1.0): -0.927410854513845 0.766116145794423"
## [1] "Casal2 cppad_casal_flags_off parameter correlation range (excluding 1.0): -0.927410854513845 0.766116145794423"
## [1] "Casal2 adolc_casal_flags_on parameter correlation range (excluding 1.0): -0.449867451595697 0.765859852647084"
## [1] "Casal2 adolc_casal_flags_off parameter correlation range (excluding 1.0): -0.475954909278459 0.77245952551618"
## [1] "Casal2 adolc_casal_flags_on_low_tol parameter correlation range (excluding 1.0): -0.450174071110356 0.76519971244179"